Table 2 |
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|
Comparison of salient features of NetPath with other popular curated signaling pathway resources |
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|
Pathway resource |
Query option for pathway molecules |
Genes transcriptionally regulated by pathway included? |
Pathways reviewed by experts? |
File formats available for download |
Textual description of reactions provided? |
Other features or comments |
|
|
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|
NetPath [5] |
Yes |
Yes |
Yes |
BioPAX, PSI-MI, SBML, Excel, Tab-delimited |
Yes |
Focus on human receptor mediated signaling. Also contains separate molecule pages with brief summary of the biology of the individual molecules |
|
BioCarta [14] |
Yes |
No |
Yes |
No download option provided |
No |
BioCarta provides commercial links to antibody reagents |
|
Science's STKE [15] |
No |
No |
Yes |
SVG |
No |
Contains species-specific and also cell-type-specific pathways |
|
KEGG [13] |
Yes |
No |
No |
KGML, BioPAX |
No |
Contains disease specific pathways |
|
Reactome [16] |
Yes |
No |
Yes |
BioPAX, SBML, PDF, SVG, Protégé, MySQL database dump |
Yes |
Also contains computationally inferred pathway reactions |
|
NCI-PID [17] |
Yes |
No |
Yes |
XML, BioPAX, SVG, JPG |
No |
Apart from NCI-Nature curated pathways, it also contains many pathways imported from BioCarta/Reactome |
|
CST [18] |
Yes |
No |
Yes (in some cases) |
|
No |
Provides pathway information along with links to protein and commercial products available for that protein |
|
WikiPathways [25] |
Yes |
No |
No |
GPML, GenMAPP, PDF, PNG, SVG |
No |
Any user can register and create a new pathway and also edit existing pathways |
|
PANTHER [26] |
Yes |
No |
Reviewed by Curation Coordinator |
SBML, SBGN, PNG |
No |
Allows community pathway curation and also provides links to Applied Biosystems genomic products |
|
|
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|
CST, Cell Signaling Technology; PID, Pathway Interaction Database; STKE, Signal Transduction Knowledge Environment. |
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|
Kandasamy et al. Genome Biology 2010 11:R3 doi:10.1186/gb-2010-11-1-r3 |
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